Bacteria and microeukaryotes are differentially segregated in sympatric wastewater microhabitats

Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream

Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.

Interactions between Bdellovibrio and like organisms and bacteria in biofilms: beyond predator-prey dynamics

Bdellovibrio and like organisms (BALOs) prey on Gram-negative bacteria in the planktonic phase as well as in biofilms, with the ability to reduce prey populations by orders of magnitude. During the last few years, evidence has mounted for a significant ecological role for BALOs, with important implications for our understanding of microbial community dynamics as well as for applications against pathogens, including drug-resistant pathogens, in medicine, agriculture and aquaculture, and in industrial settings for various uses. However, our understanding of biofilm predation by BALOs is still very fragmentary, including gaps in their effect on biofilm structure, on prey resistance, and on evolutionary outcomes of both predators and prey. Furthermore, their impact on biofilms has been shown to reach beyond predation, as they are reported to reduce biofilm structures of non-prey cells (including Gram-positive bacteria). Here, we review the available literature on BALOs in biofilms, extending known aspects to potential mechanisms employed by the predators to grow in biofilms. Within that context, we discuss the potential ecological significance and potential future utilization of the predatory and enzymatic possibilities offered by BALOs in medical, agricultural and environmental applications.

Community and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems

A fundamental question in community ecology is the role of predator-prey interactions in food-web stability and species coexistence. Although microbial microcosms offer powerful systems to investigate it, interrogating the environment is much more arduous. Here, we show in a 1-year survey that the obligate predators Bdellovibrio and like organisms (BALOs) can regulate prey populations, possibly in a density-dependent manner, in the naturally complex, species-rich environments of wastewater treatment plants. Abundant as well as rarer prey populations are affected, leading to an oscillating predatory landscape shifting at various temporal scales in which the total population remains stable. Shifts, along with differential prey range, explain co-existence of the numerous predators through niche partitioning. We validate these sequence-based findings using single-cell sorting combined with fluorescent hybridization and community sequencing. Our approach should be applicable for deciphering community interactions in other systems.

The wastewater protist Rhogostoma minus (Thecofilosea, Rhizaria) is abundant, widespread, and hosts Legionellales

Wastewater is treated by concerted actions of the microbial communities within bioreactors. Although protists (unicellular eukaryotes) are good bioindicators and important players influencing denitrification, nitrification, and flocculation, they are the least known organisms in WWTPs. The few recent environmental surveys of the protistan diversity in WWTPs show that the most abundant protistan sequences in WWTPs belong to Thecofilosea (Rhizaria). We re-investigated previously published environmental sequencing data and gathered strains from seven WWTPs to determine which species dominate WWTPs worldwide. We found that all highly abundant thecofilosean sequences represent a single species - Rhogostoma minus. Considering that Thecofilosea are frequent hosts for Legionellales, i.e. bacteria linked to waterborne diseases, we confirm that Rhogostoma minus functions as a host for Legionellales in WWTPs. Whether the highly abundant Rhogostoma minus also serves as a host for known human pathogenic Legionellales requires further attention.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Abstract

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures.

Key points

• Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga

• Comparison of the physiological features of Cand. Nitrotoga with those of other NOB

• Identification of beneficial environmental/operational parameters for proliferation

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11487-5.

Salinity is the major driver of the global eukaryotic community structure in fish-canning wastewater treatment plants

Fish-canning wastewater is characterized frequently by a high content of salt (NaCl), making its treatment particularly difficult; however, the knowledge of the effect of NaCl on eukaryotic communities is very limited. In the present study, the global diversity of eukaryotes in activated sludges (AS) from 4 different wastewater treatment plants (WWTPs) treating fish-canning effluents varying in salinity (0.47, 1.36, 1.72 and 12.76 g NaCl/L) was determined by sequencing partial 18S rRNA genes using Illumina MiSeq. A greater diversity than previously reported was observed in the AS community, which comprised 37 and 330 phylum-like and genera-like groups, respectively. In this sense, the more abundant genus-like groups (average relative abundance (RA) > 5%) were Adineta (6.80%), Lecane (16.80%), Dictyostelium (7.36%), Unclassified_Fungi7 (6.94%), Procryptobia (5.13) and Oocystis (5.07%). The eukaryotic communities shared a common core of 25 phylum-like clades (95% of total sequences); therefore, a narrow selection of the eukaryotic populations was found, despite the differences in the abiotic characteristics of fish-canning effluents and reactor operational conditions inflicted. The differences in NaCl concentration were the main factor that influenced the structure of the eukaryotic community, modulating the RAs of the different phylum-like clades of the common core. Higher levels of salt increased the RAs of Ascomycota, Chlorophyta, Choanoflagellata, Cryptophyta, Mollusca, Nematoda, Other Protists and Unclassified Fungi. Among the different eukaryotic genera here found, the RA of Oocystis (Chlorophyta) was intimately correlated to increasing NaCl concentrations and it is proposed as a bioindicator of the global eukaryotic community of fish-canning WWTPs.

Effects of the prey landscape on the fitness of the bacterial predators Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria commonly encountered in the environment. In dual predator-prey cultures, prey accessibility ensures optimal feeding and replication and rapid BALO population growth. However, the environmental prey landscape is complex, as it also incorporates non-prey cells and other particles. These may act as decoys, generating unproductive encounters which in turn may affect both predator and prey population dynamics. In this study, we hypothesized that increasing decoy:prey ratios would bring about increasing costs on the predator's reproductive fitness. We also tested the hypothesis that different BALOs and decoys would have different effects. To this end, we constructed prey landscapes including periplasmic or epibiotic predators including two types of decoy under a large range of initial decoy:prey ratio, and mixed cultures containing multiple predators and prey. We show that as decoy:prey ratios increase, the maximal predator population sizes is reduced and the time to reach it significantly increases. We found that BALOs spent less time handling non-prey (including superinfection-immune invaded prey) than prey cells, and did not differentiate between efficient and less efficient prey. This may explain why in multiple predator and prey cultures, less preferred prey appear to act as decoy.

Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter

The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.

Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata

Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.

Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant

The Seine-Morée wastewater treatment plant (SM_WWTP), with a capacity of 100,000 population-equivalents, was fed with raw domestic wastewater during all of its start-up phase. Its microbiome resulted from the spontaneous evolution of wastewater-borne microorganisms. This rare opportunity allowed us to analyze the sequential microbiota colonization and implantation follow up during the start-up phase of this WWTP by means of regular sampling carried out over 8 months until the establishment of a stable and functional ecosystem. During the study, biological nitrification–denitrification and dephosphatation occurred 68 days after the start-up of the WWTP, followed by flocs decantation 91 days later. High throughput sequencing of 18S and 16S rRNA genes was performed using Illumina's MiSeq and PGM Ion Torrent platforms respectively, generating 584,647 16S and 521,031 18S high-quality sequence rDNA reads. Analyses of 16S and 18S rDNA datasets show three colonization phases occurring concomitantly with nitrification, dephosphatation and floc development processes. Thus, we could define three microbiota profiles that sequentially colonized the SM_WWTP: the early colonizers, the late colonizers and the continuous spectrum population. Shannon and inverse Simpson diversity indices indicate that the highest microbiota diversity was reached at days 133 and 82 for prokaryotes and eukaryotes respectively; after that, the structure and complexity of the wastewater microbiome reached its functional stability. This study demonstrates that physicochemical parameters and microbial metabolic interactions are the main forces shaping microbial community structure, gradually building up and maintaining a functionally stable microbial ecosystem.